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The Phylogenetic Handbook - A Practical Approach to DNA and Protein Phylogeny
Edited by Marco Salemi and Anne-Mieke Vandamme
CUP
September 2003
Hardback 430 pages ISBN 052180390X
£45.00
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The Phylogenetic Handbook is a broad introduction to the theory and practice of nucleotide and
amino acid phylogenetic analysis. As a unique feature of this book, each chapter contains an extensive
practical section, in which step-by-step exercises on real data sets introduce the reader to the most
widely-used phylogeny software including CLUSTAL, PHYLIP, PAUP, DAMBE, TREE-PUZZLE,
TREECON, SplitsTree, TreeView, SimPlot, MEGA2, PAML, and BOOTSCANNING. Chapters
1-10 provide a strong background in basic topics such as the use of sequence databases,
alignment algorithms, tree-building methods, estimation of genetic distances, and testing models of evolution.
Additional chapters briefly survey special topics in evolution, for example modelling evolution with networks,
studying recombination, testing for positive selection, and methods in population genetics. The book will be an
invaluable resource for advanced level undergraduate and graduate students, as well as for professionals
working in the fields of molecular biology and evolution.
- Uniquely covers both the theory and practice of phylogenetic analysis
- Contains step-by-step exercises on real data sets to introduce the reader to the most widely-used
phylogeny software
- Accompanying web-site containing information about obtaining phylogeny software, datasets used
and sources of further information
Contents
1. Basic concepts of molecular evolution Anne-Mieke Vandamme;
2. Sequence databases Guy
Bottu and Marc Van Ranst;
3. Multiple alignment Des Higgins;
4. Nucleotide substitution models
Korbinian Strimmer, Arndt von Heseler and Marco Salemi;
5. Phylogeny inference based on distance models
Yves Van de Peer and Marco Salemi;
6. Phylogeny inference based on maximum liklihood methods with
TREE-PUZZLE Korbinian Strimmer and Arndt von Haeseler;
7. Phylogeny inference based on parsimony and other methods with PAUP* David L. Swofford and Jack Sullivan;
8. Phylogenetic analysis using protein sequences Fred Opperdoes;
9. Substitution rate calibration with
TREECON Yves van de Peer;
10. Selecting models of evolution David Posada;
11. Analysis of coding
sequences Yoshiyuki Suzuki and Takashi Gojobori;
12. Splits Tree: a network based tool for exploring
evolutionary relationships in molecular data Vincent Moulton;
13. Data exploration and tetrapod phylogeny
using DAMBE Xuhua Xia and Zheng Xia;
14. Detecting recombination in viral sequences Mika Salminen;
15. LAMARC: estimating population genetic parameters from molecular data Mary K. Kuhner.
To find similar publications, click on a keyword below:
Cambridge University Press
: DNA
: handbooks
: modelling, computer & mathematical
: phylogenetics
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